Deep learning in proteomics

B Wen, WF Zeng, Y Liao, Z Shi, SR Savage… - …, 2020 - Wiley Online Library
Proteomics, the study of all the proteins in biological systems, is becoming a data‐rich
science. Protein sequences and structures are comprehensively catalogued in online …

Performance measures in evaluating machine learning based bioinformatics predictors for classifications

Y Jiao, P Du - Quantitative Biology, 2016 - Springer
Background Many existing bioinformatics predictors are based on machine learning
technology. When applying these predictors in practical studies, their predictive …

GPS 5.0: an update on the prediction of kinase-specific phosphorylation sites in proteins

C Wang, H Xu, S Lin, W Deng, J Zhou… - Genomics …, 2020 - academic.oup.com
In eukaryotes, protein phosphorylation is specifically catalyzed by numerous protein kinases
(PKs), faithfully orchestrates various biological processes, and reversibly determines cellular …

MVP predicts the pathogenicity of missense variants by deep learning

H Qi, H Zhang, Y Zhao, C Chen, JJ Long… - Nature …, 2021 - nature.com
Accurate pathogenicity prediction of missense variants is critically important in genetic
studies and clinical diagnosis. Previously published prediction methods have facilitated the …

Protein kinase C controls lysosome biogenesis independently of mTORC1

Y Li, M Xu, X Ding, C Yan, Z Song, L Chen… - Nature cell …, 2016 - nature.com
Lysosomes respond to environmental cues by controlling their own biogenesis, but the
underlying mechanisms are poorly understood. Here we describe a protein kinase C (PKC) …

MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction

D Wang, S Zeng, C Xu, W Qiu, Y Liang, T Joshi… - …, 2017 - academic.oup.com
Motivation Computational methods for phosphorylation site prediction play important roles in
protein function studies and experimental design. Most existing methods are based on …

Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks

E Sebestyén, B Singh, B Miñana, A Pagès… - Genome …, 2016 - genome.cshlp.org
Alternative splicing is regulated by multiple RNA-binding proteins and influences the
expression of most eukaryotic genes. However, the role of this process in human disease …

GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins

M Chen, W Zhang, Y Gou, D Xu, Y Wei… - Nucleic acids …, 2023 - academic.oup.com
Protein phosphorylation, catalyzed by protein kinases (PKs), is one of the most important
post-translational modifications (PTMs), and involved in regulating almost all of biological …

Best practices for bioinformatic characterization of neoantigens for clinical utility

MM Richters, H Xia, KM Campbell, WE Gillanders… - Genome medicine, 2019 - Springer
Neoantigens are newly formed peptides created from somatic mutations that are capable of
inducing tumor-specific T cell recognition. Recently, researchers and clinicians have …

New perspectives, opportunities, and challenges in exploring the human protein kinome

LJ Wilson, A Linley, DE Hammond, FE Hood… - Cancer research, 2018 - AACR
The human protein kinome comprises 535 proteins that, with the exception of approximately
50 pseudokinases, control intracellular signaling networks by catalyzing the phosphorylation …